2I7D

Structure of Human cytosolic deoxyribonucleotidase in complex with deoxyuridine, AlF4 and Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of Human and Murine cytosolic deoxyribonucleotidase: Insights into substrate specificity and catalysis

Wallden, K.Rinaldo-Matthis, A.Ruzzenente, B.Rampazzo, C.Bianchi, V.Nordlund, P.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'(3')-deoxyribonucleotidase, cytosolic type
A, B
193Homo sapiensMutation(s): 0 
Gene Names: NT5C (DNT1, UMPH2)
EC: 3.1.3.-
Find proteins for Q8TCD5 (Homo sapiens)
Go to Gene View: NT5C
Go to UniProtKB:  Q8TCD5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ALF
Query on ALF

Download SDF File 
Download CCD File 
A, B
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DUR
Query on DUR

Download SDF File 
Download CCD File 
A, B
2'-DEOXYURIDINE
C9 H12 N2 O5
MXHRCPNRJAMMIM-SHYZEUOFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.166 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 39.623α = 68.92
b = 47.153β = 81.69
c = 62.384γ = 74.99
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
XSCALEdata scaling
PDB_EXTRACTdata extraction
CNSphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance